R/Pharma Summit @ Posit Conf 2024, August 11th
Slides available: pharmar.github.io/events-positconf2024
On behalf of the R Validation Hub team:
Aaron Clark Arcus Biosciences
Doug Kelkhoff Roche
The R Validation Hub is a collaboration to support the adoption of R within a biopharmaceutical regulatory setting (pharmaR.org)
Works with and provides support to the R Foundation and to the key organizations developing, maintaining, distributing and using R software
Over USD $1.4 Million
R Validation Hub, R-Ladies
Stanford Data Institute
R/Medicine, R/Pharma, useR!, LatinR, and more
Guidance on compliant use of R and management of packages
Building a public, validation-ready resource for R packages
Coline Zeballos
Connecting validation experts across the industry
Jaxon Abercrombie, Anuja Das, Antal Martinecz
{riskmetric}Gather and report on risk heuristics to support validation decision-making
Eric Milliman
{riskassessment}A web interface to {riskmetric}, supporting review, annotation and cataloging of decisions
Aaron Clark, Jeff Thompson
Keep your hand raised if…
{riskmetric}, {riskassessment}){riskassessment} App Workstream 5min{riskmetric} workstream 10min.R files through their eSUB portal2.Next date: 🗓️ Aug 20, 2024
Speaker: 👷♂️ Bríd Roberts, Novartis [TODO: how do I change this icon to female?]
Topic:
The Software Open Source (SOS) team manages and executes the risk assessment process for R package validation at Novartis. The team uses an internally developed R package to classify the risk of each package as “low”, “medium”, or “high”.
We analysed the risk assessment data over two time points to determine the impact on the assigned risk categorisation for packages with AND without version changes.
In this talk, we showcase the risk assessments over time, the causes of any risk class changes, and their impact on various teams within our organizations as a result.
Then: Outdated, clumsy, hard to navigate… Insert Image TODO
Now: Update, streamlined, user friendly! Insert Image TODO
{riskassessment} App{riskassessment} AppExpanded decision automation to include individual {riskmetric} assessment values
New Function Explorer page and faster exploration of source code
Expanded the package dependency view
Miscellaneous items
About tabshinymanager deploymentThe feedback loop is crucial! All of these improvements started off as community-driven suggestions on our GitHub repo. If you have an idea that doesn’t already exist on the existing list of issues, submit a new issue today and it may become a reality tomorrow.
{riskassessment} AppTODO: add link and icon for small car
https://app.pharmar.org/riskassessment/
Looking for Volunteer “Leads” to represent
{riskassessment} App{riskassessment} App{riskassessment} App{riskmetric}{riskmetric} RoadmapRunning from risk scores & focusing solely on metric assessments
oyster, srr, pkgstats, etc)Supporting a transparent, open, dynamic, cross-industry approach of establishing and maintaining a repository of R packages.
In close communication with many beloved R projects
pharmaversetargetting repos integration
r-lib/paktargetting pak integration
focus on proving capabilities, quick development
✨ all modelled after r-hub/repos
repo <- "https://raw.githubusercontent.com/pharmaR/repos/main/ubuntu-22.04/4.5"
options(repos = c("pharmaR/repos/ubuntu" = repo))
available.packages()options(
available_packages_filters = risk_filter(
# package is exceptionally testing
(quality_code_coverage >= 0.8 &
quality_example_coverage >= 0.8 &
quality_r_cmd_check_errors == 0) |
# or is exceptionally well adopted
(percentile(quality_downloads_1yr) > 90 |
quality_reverse_dependencies_count >= 10) |
# or seems to follow thorough development practices
(quality_has_website &
quality_vignette_count >= 1 &
quality_author_count >= 3)
)
)*aspirational deviations from proof of concept in github.com/pharmaR/pharmapkgs
DownloadURL)pak::pkg_installDCF file forked from r-hub/repos
Package: bslib
Version: 0.6.1
Depends: R (>= 2.10), R (>= 4.4), R (< 4.4.99)
License: MIT + file LICENSE
DownloadURL:
https://github.com/cran/bslib/releases/download/0.6.1/bslib_0.6.1_b4_R4.4_x86_64-pc-linux-gnu-ubuntu-22.04.tar.gz
Built: R 4.4.0; ; 2023-11-29 16:39:06 UTC; unix
RVersion: 4.4
Platform: x86_64-pc-linux-gnu-ubuntu-22.04
Imports: base64enc, cachem, grDevices, htmltools (>= 0.5.7), jquerylib (>= 0.1.3),
jsonlite, lifecycle, memoise (>= 2.0.1), mime, rlang, sass (>= 0.4.0)
...Added fields for risk-based assessment
Calculates package QA metadata on updated packages and their reverse dependencies
Produces logs and other reproducibility data
In the future: can run on in-house infrastructure
Automating up-to-date quality metrics to support sponsor risk assessment
Should mimic environments of companies and health authority reviewers
To be used by the Regulatory R Repository for packages cohort validation
Main intent: start a cross-company dialogue on infrastructure